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Identical Novel Beta Coronavirus Sequences Signal H2H
Recombinomics Commentary 21:00
November 30, 2012

A paper “Recovery from severe coronavirus infection” published in the Saudi Med J by Dr Ziad Memesh and colleagues describes the third confirmed novel betacornavirus case (45M), which was announced by the Kingdom of Saudi Arabia Ministry of Health on November 4, the date of discharge.
The case is a gym-teacher from Riyadh, Saudi Arabia who developed symptoms on October 9. His conditioned worsened and he visited the emergency room on October 10 and 12. His conditioned continued to worsen and was intubated for mechanical ventilation on October 13 and transferred to the ICU. Kidney failure led to hemodialysis between October 15-23.
The novel betacornavirus was detected in respiratory samples using PCR tests for the upstream region of the E gene as well as ORF1B and N genes. The paper included two sets of sequences for two regions, a 311 Bp fragment of ORF1B (positions 18105-18414) and a 409 BP fragment of E (positions 27278-27868).  These sequences were from samples collected from case 1 (60M businessman from Bisha, treated in Jeddah, confirmed at Erasmus Medical Center in the Netherlands) and case 3 described above. The two sets of sequences were identical to the updated public sequence for case 1 (JX869059.2) as well as case 2 (49M businessman from Doha, Qatar and treated in London).
The identity of the two regions in all three cases once again indicates these cases were not infected by an animal source.  Media reports continue to cite the relatedness to bat coronaviruses, which were identified under an enhanced surveillance program to identify the natural reservoir for SARS CoV.  Bats were found to host a wide variety of coronaviruses including the two members of class 2c found in Guangdong Province, China (HKU4 and HKU5).  These cases were identified using the same pan-coronavirus PCR tested used to identify the first two recent human cases.  However, for the two regions above the three cases from widely separated areas in two countries (Bisha, Doha, Riyadh) were identical, yet had more than 20% mismatches for the most closely related bat class 2c coronaviruses (HKU4 and HKU5).
Moreover, WHO has now reported two confirmed cases from an ICU outbreak in Zarka, Jordan in April.  The novel betacornavirus spread throughout the unit and infected at least seven nurses and a doctor as well as the brother of a fatally infected nurse.  The ECDC report cited one fatality, but WHO has already confirmed two fatalities.
Release of sequences from the Jordan outbreak would be useful.

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